ABSTRACT Endometriosis is a highly prevalent gynecologic disease characterized by severe pelvic pain and infertility that negatively impacts the wellbeing and quality of life of millions of women worldwide (1, 2). Despite decades of basic and clinical research on endometriosis, there is limited understanding of its pathophysiology and no specific, non-invasive diagnostic assays are available (3, 4). As a result, diagnosis can only be made via a surgical procedure (e.g., laparoscopy), significant delays in diagnosis have been reported (in average of 7 years since onset of symptoms), and there is still no definitive cure (5). We have recently applied an innovative, high throughput human protein chip-based platform to the discovery of the serum autoimmune component of endometriosis patients and controls. Using CDI's HuProt? protein microarray v2 containing over 19,000 yeast-derived recombinant human proteins we decoded the antigen specificity of auto-antibodies (AAbs) present at different levels in sera of women with endometriosis compared to controls. We have identified 166 AAbs that are present at higher or lower levels in sera from women with endometriosis compared to controls and that could be used as the basis of a non-invasive immune-based diagnostic assay. We now propose to validate our findings by testing a larger cohort of samples using a focused protein array based on the differentially expressed AAbs, and to determine the usefulness of the final panel as a non-invasive diagnostic test for endometriosis. The long-term goal of this STTR Phase I study is to fill an important void in the clinical management of women with pelvic pain and/or infertility (6-8) by developing a non-invasive diagnostic assay for endometriosis. We propose to address this goal via one specific aim: to assess the diagnostic potential of AAbs identified during the discovery phase on a larger sample set of patients and controls already available from the Ponce School of Medicine (PSM) Endometriosis Research Program (ERP)'s biobank consisting of biospecimens and data from Puerto Rican subjects. For that purpose, we will construct a focused array (mini-chip) of human autoantigens selected based on the 100 most differentially detected AAbs in the sera of women with endometriosis compared to controls, and will conduct a retrospective validation study by analyzing serum samples from a larger cohort of patients and controls. These data will serve to 1- refine the number of biomarkers that maintain their high discriminatory power, and 2- will support the use of these focused mini- chips as a diagnostic tool to be used in clinical settings. In Phase 2, we will propose to expand the validation of these potential biomarkers by utilizing the focused-array approach to include sera from patients from other research cohorts to increase the ethnic coverage of the test, utilizing at least one or more of the biomarkers identified in Phase I, and to explore other more cost-effective and practical assay formats. Development of specific, non-invasive tests to allow identification of women with pelvic pain and/or infertility at risk of having endometriosis using an easily obtainable serum sample is of high priority in the Women's Health/Gynecology fields given the high prevalence of pelvic pain and endometriosis among women of reproductive age, and the risk of complications (disease progression beyond the pelvis, hysterectomy, infertility, ovarian cancer) in those not promptly diagnosed and treated. KEYWORDS: Endometriosis, Diagnostics, Non-invasive diagnosis, Autoimmunity, Autoantibodies, Autoantigens, Protein Microarrays, Multiplex, High Throughout, Proteomics, Pelvic Pain, Women's Health